Computational protocol: The different expressed serum proteins in rhCygb treated rat model of liver fibrosis by the optimized two-dimensional gel electrophoresis

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Protocol publication

[…] Two dimensional gels were stained with the silver method to make it compatible with mass spectrometry. The stained gels were scanned using UMax Magic scan (Amersham Biosciences, Sweden), and analyzed with PDQuest 8.0.1 (Bio-Rad). In-gel digestion and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for identification of different proteinsanalysis were performed at the Beijing Genomics Institute in Shenzhen, China. Combined peptide mass fingerprinting (PMF) and tandem mass spectrometry (MS/MS) queries were searched against the NCBI database, using the MASCOT search engine from Matrix Science ( to identify the proteins. Proteins matching more than five peptides and with a MASCOT score higher than 60 were considered significant (p < 0.05). […]

Pipeline specifications

Software tools PDQuest 2-D, Mascot Server
Application MS-based untargeted proteomics
Organisms Rattus norvegicus, Homo sapiens
Diseases Liver Cirrhosis, Liver Diseases